How to Sanitize Your Sponge Germa-phobes unite! Here’s a quick way to sanitize your sponge in the microwave. Pinterest Facebook Twitter Email This handy dandy trick kills 99% of the bacteria. This handy dandy trick kills 99% of the bacteria. Wet the sponge and pop it in the microwave on a paper towel. Place a small bowl of water next to it to protect the microwave. Put it on high for one minute, and voila! Bye-bye, bacteria.